Mac-OS-X-Installation.md

Installing ISMRMRD, Gadgetron, Siemens converter, and GE tools on Mac OS X.

This is the Homebrew version of the installation:

• /usr/local is owned by the main user
• root (and sudo) are not used
• Homebrew's python 2.7 is installed
• Using Matlab R2015b
• GPU features are NOT supported

Prerequisites

0. Install Xcode

1. Install OS X Command Line Tools on the terminal:

   xcode-select --install

2. Install Homebrew and check that it's working. On Mac OS X 10.11.2 (El Capitan), the permissions/ownership of some folders in /usr/local/ can be changed by the OS. Use brew doctor to check and follow their suggestions for changing ownership. (May happen more than once during installation.)

3. Set environment variables in ~/.bash_profile or its equivalent

   # Put homebrew paths first
   export PATH=/usr/local/bin:/usr/local/sbin:$PATH
   
   # Python
   export PYTHONHOME=/usr/local/Frameworks/Python.framework/Versions/2.7
   
   # MATLAB, ISMRMRD, GADGETRON
   export MATLAB_HOME=/Applications/MATLAB_R2015b.app
   export ISMRMRD_HOME=/usr/local
   export GADGETRON_HOME=/usr/local
   
   export PATH=$MATLAB_HOME/bin:$PATH
   export PATH=$ISMRMRD_HOME/bin:$PATH
   export PATH=$GADGETRON_HOME/bin:$PATH
   
   export DYLD_FALLBACK_LIBRARY_PATH=$ISMRMRD_HOME/lib:$DYLD_FALLBACK_LIBRARY_PATH
   export DYLD_FALLBACK_LIBRARY_PATH=$GADGETRON_HOME/lib:$DYLD_FALLBACK_LIBRARY_PATH
   export DYLD_FALLBACK_LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH:$MATLAB_HOME/bin/maci64
   

4. Add the brew science formulae and the python formulae

    brew tap homebrew/science
    brew tap Homebrew/python
   

5. Install ISMRMRD and Gadgetron dependencies

    brew install wget cmake boost qt fftw swig glew ace armadillo dcmtk doxygen docbook-xsl fop
    brew install hdf5 --enable-cxx
   
    brew install python boost-python numpy scipy
    brew install matplotlib --with-pygtk --with-pyqt
    brew install libxml2 --with-python
   
    pip install h5py PyXB
   

6. Install ISMRMRD Python API:

   git clone https://github.com/ismrmrd/ismrmrd-python
   cd ismrmrd-python
   python setup.py install
   

7. Install ISMRMRD Python Tools:

    git clone https://github.com/ismrmrd/ismrmrd-python-tools
    cd ismrmrd-python-tools
    python setup.py install
   

8. Install GTest

   wget https://github.com/google/googletest/archive/release-1.7.0.tar.gz
   tar xzf release-1.7.0.tar.gz
   cd googletest-release-1.7.0
   cp -r include/gtest /usr/local/include/
   mkdir build
   cd build
   cmake ..
   make
   cp libgtest* /usr/local/lib/
   

9. Future Step: Install CUDA and CULA

Installation from Sources

ISMRMRD

git clone https://github.com/ismrmrd/ismrmrd
cd ismrmrd
mkdir build
cd build/
cmake -D CMAKE_INSTALL_PREFIX=$ISMRMRD_HOME ../
make
make install

Gadgetron

git clone https://github.com/gadgetron/gadgetron
cd gadgetron
mkdir build
cd build/
cmake -D CMAKE_INSTALL_PREFIX=$GADGETRON_HOME -D PYTHON_LIBRARY=`python-config --prefix`/Python -D PYTHON_INCLUDE_DIR=`python-config --prefix`/Headers ../
make
make install

Siemens converter (needed for Gadgetron integration tests)

git clone https://github.com/ismrmrd/siemens_to_ismrmrd
cd siemens_to_ismrmrd
mkdir build
cd build/
cmake -D CMAKE_INSTALL_PREFIX=$ISMRMRD_HOME ../
make
make install

GE tools (optional)

git clone https://github.com/nih-fmrif/ge-tools
cd ge-tools
mkdir build
cd build/
cmake -D CMAKE_INSTALL_PREFIX=$ISMRMRD_HOME ../
make
make install

Post-install Config and Testing

0. Copy $GADGETRON_HOME/share/gadgetron/config/gadgetron.xml.example to $GADGETRON_HOME/share/gadgetron/config/gadgetron.xml

1. Fetch Gadgetron test data: run python get_data.py in test/integration in the Gadgetron source tree. Re run if this times out.

2. Run integration tests: run python run_all_tests.py test_cases.txt in test/integration in the Gadgetron source tree.